rs2468168

chr8-119157399-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_928585.3(LOC105375725):n.86+5320T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 152,100 control chromosomes in the GnomAD database, including 40,001 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.72 (40001 hom., cov: 32)
• Consequence: LOC105375725 XR_928585.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.12

Genes affected

LOC105375725 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375725	XR_928585.3	n.86+5320T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108932 AN: 151982 Hom.: 39949 Cov.: 32

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.736

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.717 AC: 109037 AN: 152100 Hom.: 40001 Cov.: 32 AF XY: 0.713 AC XY: 53035 AN XY: 74348

Gnomad4 AFR AF: 0.875

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.689

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.740

Alfa AF: 0.605 Hom.: 1928

Bravo AF: 0.722

Asia WGS AF: 0.706 AC: 2461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.0040
Dann	Benign	0.26

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2468168; hg19: chr8-120169638;